<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
  <model id="Model4" name="Case Study 1, Model 4 (overcomplicated)">
    <listOfCompartments>
      <compartment id="compartment" name="compartment" size="1"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="S" name="S" compartment="compartment" initialConcentration="1"/>
      <species id="dS" name="dS" compartment="compartment" initialConcentration="0"/>
      <species id="R" name="R" compartment="compartment" initialConcentration="1"/>
      <species id="RS" name="RS" compartment="compartment" initialConcentration="0"/>
      <species id="Rpp" name="Rpp" compartment="compartment" initialConcentration="0"/>
      <species id="PhA" name="PhA" compartment="compartment" initialConcentration="1"/>
      <species id="RppPhA" name="RppPhA" compartment="compartment" initialConcentration="0"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="Noise" value="0.06"/>
    </listOfParameters>
    <listOfReactions>
      <reaction id="reaction_0" name="R1" reversible="false">
        <listOfReactants>
          <speciesReference species="S"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="dS"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment </ci>
              <ci> k1 </ci>
              <ci> S </ci>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="k1" value="0.05"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_1" name="R2">
        <listOfReactants>
          <speciesReference species="R"/>
          <speciesReference species="S"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="RS"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment </ci>
              <apply>
                <minus/>
                <apply>
                  <times/>
                  <ci> k1 </ci>
                  <ci> R </ci>
                  <ci> S </ci>
                </apply>
                <apply>
                  <times/>
                  <ci> k2 </ci>
                  <ci> RS </ci>
                </apply>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="k1" value="0.4"/>
            <parameter id="k2" value="0.02"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_2" name="R3" reversible="false">
        <listOfReactants>
          <speciesReference species="RS"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="Rpp"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment </ci>
              <ci> k1 </ci>
              <ci> RS </ci>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="k1" value="0.4"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_3" name="R4">
        <listOfReactants>
          <speciesReference species="Rpp"/>
          <speciesReference species="PhA"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="RppPhA"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment </ci>
              <apply>
                <minus/>
                <apply>
                  <times/>
                  <ci> k1 </ci>
                  <ci> Rpp </ci>
                  <ci> PhA </ci>
                </apply>
                <apply>
                  <times/>
                  <ci> k2 </ci>
                  <ci> RppPhA </ci>
                </apply>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="k1" value="0.01"/>
            <parameter id="k2" value="0.005"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_4" name="R5" reversible="false">
        <listOfReactants>
          <speciesReference species="RppPhA"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="R"/>
          <speciesReference species="PhA"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment </ci>
              <ci> k1 </ci>
              <ci> RppPhA </ci>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="k1" value="0.005"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>
